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Reposted by Assaf Zaritsky

Rita Strack @ritastrack.bsky.social · 14d

Nature Biomedical Engineering is hiring again! This time we're hoping to add an editor with machine learning expertise to the team (although we are open to those with other relevant expertise!) Deadline is Oct 20. Please RT! springernature.wd3.myworkdayjobs.com/SpringerNatu...

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Reposted by Assaf Zaritsky

Janelia Research Campus @hhmijanelia.bsky.social · Aug 26

📢We're #hiring Group Leaders!

Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.

🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines

Apply by Nov. 4👉 https://janelia.link/groupleader

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Reposted by Assaf Zaritsky

Nicoletta Petridou @nicolettapetridou.bsky.social · Aug 8

We are searching for an enthusiastic scientist to join our team and establish annual killifish as a model system for early developmental biology and biophysics! @embl.org @embldbunit.bsky.social

Apply here:
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...

Please re-post 🙏

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Reposted by Assaf Zaritsky

Allen Institute @alleninstitute.org · Jul 8

How do organelles change over the course of a stem cell’s life?

ADIs @cohenlaboratory.bsky.social, @assafzaritsky.bsky.social , and @mattersoflight.bsky.social are using ML and cell engineering to explore the #FrontierScience of stem cell differentiation.
alleninstitute.org/division/fro...

Data-driven modeling of inter-organelle dynamic interactions throughout differentiation with multispectral and label free live imaging

With funding from the Allen Distinguished Investigators program, these investigators hypothesize that complex and dynamic patterns of organelle connection and communication are distinctive across diff...

alleninstitute.org

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Reposted by Assaf Zaritsky

Peter O'Toole @yorkbioimaging.bsky.social · Jul 1

BIG start to #mmc2025 with Assaf Zaritsky giving an awesome opening plenary.

@royalmicrosoc.bsky.social @eurobioimaging.bsky.social @globias.bsky.social @bioimaginguk.bsky.social @globalbioimaging.bsky.social

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

Sorry, I meant @leeat-keren.bsky.social and Yael Amitay....

Assaf Zaritsky @assafzaritsky.bsky.social · May 9

A creative and technically challenging idea led by @zamir_amos, with key contributions from Yuval Tamir and @yaelam75. This would not have been possible without the great collaboration with @leeat_keren! And thanks to @WellcomeLeap ΔTissue for funding!

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

CISM source code is publicly available github.com/zaritskylab/...

Also, check CISM’s backbone FANMOD+, that enables efficient motifs extraction in “multi-colored” networks github.com/zaritskylab/...

Try it out!

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GitHub - zaritskylab/CISM: A two-step method to identify local interconnected cell structures associated with a disease state in single cell spatial proteomics data

A two-step method to identify local interconnected cell structures associated with a disease state in single cell spatial proteomics data - zaritskylab/CISM

github.com

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

Our results suggest that the local organization of a few cells in discriminative motifs are emergent properties that may define an intermediate spatial scale driving tissue function

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

CISM’s unsupervised motif enumeration followed by supervised context-dependent selection distils the discriminative motifs from the huge and noisy landscape of all putative sub-networks of intercellular interactions and provides discrimination along with interpretability

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

To demonstrate the general applicability of CISM for identifying local cellular structures linked to disease states, we applied it to investigate the tumor microenvironment in a human cohort of Breast Cancer (TNBC) patients, comparing short-term and long-term survivors.

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

The same motifs can be differentially analyzed according to different context-dependent selection of the discriminative motifs. We demonstrate this by investigating the immune microenvironment of NP versus PN (metastatic lymph nodes that did not develop distant metastases)

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

Spatial interpretation of motifs localization patterns reveals an association between (local) motifs to (global) tissue compartments highlighting the potential contribution of CISM to multi-scale analysis and interpretation

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

The spatial arrangement of cell types within the discriminative motifs contributed to disease state classification, indicating that the specific intra-motif cell-cell interactions are sensitive markers for disease state beyond their cell type composition

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

Exploring the landscape of the discriminative motifs-induced cell distribution and motifs-induced pairwise cell-cell interactions revealed differential composition of cell type and cell-cell interactions

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

Classifying NN vs. NP disease states using discriminative four-cell motifs outperformed other methods, suggesting that these motifs can act as multicellular signatures of disease

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

We applied CISM to investigate future metastases by analyzing the immune microenvironment in tumor-free lymph nodes of melanoma patients using multiplexed imaging.

Cohort and data by our collaborators @yaelam75 and @leeat_keren are described here doi.org/10.1101/2024...

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

These discriminative motifs’ representations can be interpreted based on their prevalence, contribution to classification, identity of the cells that comprise them and their pairwise interactions and their spatial location in respect to more global tissue compartments

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

CISM context-dependent discriminative motifs can be used to formulate a machine learning-based prediction of the tissue’s disease state where each patient is represented by the (sparse) vector of its discriminative motifs' frequencies

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

CISM reduces the number of potential high-order interactions with unsupervised selection of ‘motifs’, enriched local multicellular structures, and then associates these motifs with the tissue disease state according to their presence in patients at different clinical states

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

The clinical manifestation of diseased tissue arises from intricate intercellular interactions that extend beyond pairwise cell-cell interactions. Deciphering these processes is challenging due to the combinatorial complexity of multicellular organization.

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Source: https://doi.org/10.15252/msb.202110726

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Assaf Zaritsky @assafzaritsky.bsky.social · May 9

Super excited to share our new method: Context-dependent Identification of Spatial Motifs (CISM)! 🚀 A two-step approach for uncovering fine-scale intercellular modules associated with human disease states from single-cell spatial data.

doi.org/10.1101/2025...

🧵

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Reposted by Assaf Zaritsky

Allen Institute @alleninstitute.org · May 1

Unveiling crucial insights into nuclear growth in hiPSC colonies. By analyzing 3D timelapse data, our Cell Science team has shown how cell lineage & environment shape cellular behavior.

This timelapse illuminates the height of nuclei from 4μm (turquoise) to 11μm (fuchsia). 🔗👇

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Assaf Zaritsky @assafzaritsky.bsky.social · May 1

MBoC (@ascbiology.bsky.social Society Journal) is Looking for Early-Career Editorial Board Members!

www.ascb.org/society-news...

Submit your application by May 22, 2025!

MBoC is Looking for Early-Career Editorial Board Members — Join Us! - ASCB

Are you a senior postdoc or early-career faculty member who’s passionate about publishing, peer review, and amplifying great science? We’d love for you to consider joining the Molecular Biology of the...

www.ascb.org

Reposted by Assaf Zaritsky

Dave Barry @david-j-barry.bsky.social · Apr 17

"This symposium explores the power of microscopy imaging as a data-rich resource for quantifying cellular phenotypes, with a strong focus on high-content imaging techniques such as Cell Painting and their applications in drug discovery and basic cell biology"

cytodata25.eu-openscreen.eu

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